Bern's positioning strategies: Escaping the fate of a secondary capital city?

Bern is a classic example of a so-called secondary capital city, which is defined as a capital city that is not the primary economic center of its nation. Such capital cities feature a specific political economy characterized by a strong government presence in its regional economy and its local governance arrangements. Bern has been losing importance in the Swiss urban system over the past decades due to a stagnating economy, population decline and missed opportunities for regional cooperation. To re-position itself in the Swiss urban hierarchy, political leaders and policymakers established a non-profit organization called “Capital Region Switzerland” in 2010 arguing that a capital city should not be measured by economic success only, but by its function as a political center where political decisions are negotiated and implemented. This city profile analyses Bern's strategy and discusses its ambitions and limitations in the context of the city's history, socio-economic and political conditions. We conclude that Bern's positioning strategy has so far been a political success, yet that there are severe limitations regarding advancing economic development. As a result, this re-positioning strategy is not able to address the fundamental economic development challenges that Bern faces as a secondary capital city.

Nonlesions, misdiagnoses, missed diagnoses, and other interpretive challenges in fish histopathology studies: a guide for investigators, authors, reviewers, and readers.

Differentiating salient histopathologic changes from normal anatomic features or tissue artifacts can be decidedly challenging, especially for the novice fish pathologist. As a consequence, findings of questionable accuracy may be reported inadvertently, and the potential negative impacts of publishing inaccurate histopathologic interpretations are not always fully appreciated. The objectives of this article are to illustrate a number of specific morphologic findings in commonly examined fish tissues (e.g., gills, liver, kidney, and gonads) that are frequently either misdiagnosed or underdiagnosed, and to address related issues involving the interpretation of histopathologic data. To enhance the utility of this article as a guide, photomicrographs of normal and abnormal specimens are presented. General recommendations for generating and publishing results from histopathology studies are additionally provided. It is hoped that the furnished information will be a useful resource for manuscript generation, by helping authors, reviewers, and readers to critically assess fish histopathologic data.

The social perception of heroes and murders: Effects of gender-inclusive language in media reports

The way media depict women and men can reinforce or diminish gender stereotyping. Which part does language play in this context? Are roles perceived as more gender-balanced when feminine role nouns are used in addition to masculine ones? Research on gender-inclusive language shows that the use of feminine-masculine word pairs tends to increase the visibility of women in various social roles. For example, when speakers of German were asked to name their favorite "heroine or hero in a novel," they listed more female characters than when asked to name their favorite "hero in a novel." The research reported in this article examines how the use of gender-inclusive language in news reports affects readers' own usage of such forms as well as their mental representation of women and men in the respective roles. In the main experiment, German participants (N = 256) read short reports about heroes or murderers which contained either masculine generics or gender-inclusive forms (feminine-masculine word pairs). Gender-inclusive forms enhanced participants' own usage of gender-inclusive language and this resulted in more gender-balanced mental representations of these roles. Reading about "heroines and heroes" made participants assume a higher percentage of women among persons performing heroic acts than reading about "heroes" only, but there was no such effect for murderers. A post-test suggested that this might be due to a higher accessibility of female exemplars in the category heroes than in the category murderers. Importantly, the influence of gender-inclusive language on the perceived percentage of women in a role was mediated by speakers' own usage of inclusive forms. This suggests that people who encounter gender-inclusive forms and are given an opportunity to use them, use them more themselves and in turn have more gender-balanced mental representations of social roles.

The sequence comparison index: A novel method for comparing proteins and proteomes

Historically morphological features were used as the primary means to classify organisms. However, the age of molecular genetics has allowed us to approach this field from the perspective of the organism's genetic code. Early work used highly conserved sequences, such as ribosomal RNA. The increasing number of complete genomes in the public data repositories provides the opportunity to look not only at a single gene, but at organisms' entire parts list. ^ Here the Sequence Comparison Index (SCI) and the Organism Comparison Index (OCI), algorithms and methods to compare proteins and proteomes, are presented. The complete proteomes of 104 sequenced organisms were compared. Over 280 million full Smith-Waterman alignments were performed on sequence pairs which had a reasonable expectation of being related. From these alignments a whole proteome phylogenetic tree was constructed. This method was also used to compare the small subunit (SSU) rRNA from each organism and a tree constructed from these results. The SSU rRNA tree by the SCI/OCI method looks very much like accepted SSU rRNA trees from sources such as the Ribosomal Database Project, thus validating the method. The SCI/OCI proteome tree showed a number of small but significant differences when compared to the SSU rRNA tree and proteome trees constructed by other methods. Horizontal gene transfer does not appear to affect the SCI/OCI trees until the transferred genes make up a large portion of the proteome. ^ As part of this work, the Database of Related Local Alignments (DaRLA) was created and contains over 81 million rows of sequence alignment information. DaRLA, while primarily used to build the whole proteome trees, can also be applied shared gene content analysis, gene order analysis, and creating individual protein trees. ^ Finally, the standard BLAST method for analyzing shared gene content was compared to the SCI method using 4 spirochetes. The SCI system performed flawlessly, finding all proteins from one organism against itself and finding all the ribosomal proteins between organisms. The BLAST system missed some proteins from its respective organism and failed to detect small ribosomal proteins between organisms. ^

Gay Parenthood and the Revolution of the Modern Family: An Examination of the Unique Barriers Confronting Gay Adoptive Parents

Abstract: In recent decades, the structure of the American family has been revolutionized to incorporate families of diverse and unconventional compositions. Gay and lesbian couples have undoubtedly played a crucial role in this revolution by establishing families through the tool of adoption. Eleven adoptive parents from the state of Connecticut were interviewed to better conceptualize the unique barriers gay couples encounter in the process adoption. Both the scholarly research and the interview data illustrate that although gay couples face enormous legal barriers, the majority of their hardship comes through social interactions. As a result, the cultural myths and legal restrictions that create social hardships for gay adoptive parents forge a vicious and discriminatory cycle of marginalization that American legal history illustrates is best remedied through judicial intervention at the Supreme Court level. While judicial intervention, alone, cannot change the reality of gay parenthood, I argue that past judicial precedent illustrates that such change can serve as a tool of individual, political, and legal validation for the gay community for obtaining equal rights.

Incident hypertension among pre-hypertensive adolescents: Evaluation of pre-hypertension as an independent risk factor among secondary school students in the Houston area

Cardiovascular disease has been the leading cause of death in the United States for over fifty years. While multiple risk factors for cardiovascular disease have been identified, hypertension is one of the most commonly recognized and treatable. Recent studies indicate that the prevalence of hypertension among children and adolescents is between 3-5%, much higher than originally estimated and likely rising due to the epidemic of obesity in the U.S. In 2004, the National High Blood Pressure Education Program Working Group on High Blood Pressure in Children and Adolescents published new guidelines for the diagnosis and treatment of hypertension in this population. Included in these recommendations was the creation of a new diagnosis, pre-hypertension, aimed at identifying children at-risk for hypertension to provide early lifestyle interventions in an effort to prevent its ultimate development. In order to determine the risk associated with pre-hypertension for the development of incident HTN, a secondary analysis of a repeated cross-sectional study measuring blood pressure in Houston area adolescents from 2000 to 2007 was performed. Of 1006 students participating in the blood pressure screening on more than one occasion not diagnosed with hypertension at initial encounter, eleven were later found to have hypertension providing an overall incident rate of 0.5% per year. Incidence rates were higher among overweight adolescents–1.9% per year [IRR 8.6 (1.97, 51.63)]; students “at-risk for hypertension” (pre-hypertensive or initial blood pressure in the hypertensive range but falling on subsequent measures)–1.4% per year [IRR 4.77 (1.21, 19.78)]; and those with blood pressure ≥90th percentile on three occasions–6.6% per year [IRR 21.87 (3.40, 112.40)]. Students with pre-hypertension as currently defined by the Task Force did have an increased rate of hypertension (1.1% per year) but it did not reach statistical significance [IRR 2.44 (0.42, 10.18)]. Further research is needed to determine the morbidity and mortality associated with pre-hypertension in this age group as well as the effectiveness of various interventions for preventing the development of hypertensive disease among these at-risk individuals. ^

The association between maternal use of spermicides, condoms, intra-uterine devices or progesterone and major structural birth defects

Birth defects occur in 1 of every 33 babies born in the United States, and are the leading cause of infant death. Mothers using contraceptives that become pregnant may continue to use their contraceptives after their first missed menstrual period, thus exposing their baby in utero to the contraceptive product. Progesterone is also sometimes prescribed during the first trimester of pregnancy to mothers with a history of miscarriages or infertility problems. To ensure the safety of these products, it is important to investigate whether there is an increased occurrence of babies born with birth defects to mothers using various contraceptive methods or progesterone in early pregnancy. Using data from the National Birth Defects Prevention Study (NBDPS), an ongoing multi-state, population based case-control study, this study assessed maternal exposures to IUDs, spermicides, condoms and progesterone in early pregnancy. ^ Progesterone used for threatened miscarriage during the first three months of pregnancy was associated with an increased occurrence of hypoplastic left heart (adjusted odds ratios (OR) 2.24, 95% CI 1.13-4.21), perimembranous ventricular septal defects (OR 1.64, 95% CI 1.10-2.41), septal associations (OR 2.52, 95% CI 1.45-4.24), esophageal atresia (OR 1.82, 95% CI 1.04-3.08), and hypospadias (OR 2.12, 95% CI 1.41-3.18). Mothers using progesterone for injectable contraception had increased (OR > 2.5), but insignificant odds ratios for anencephaly, septal associations, small intestinal atresias and omphalocel. Progesterone used for fertility was not associated with an increased occurrence of any birth defects examined. ^ Mothers using progesterone for fertility assistance and threatened miscarriage were very similar with respect to their demographics and pregnancy history. They also both reported similar types of progesterone. Thus, if progesterone was a causal risk factor for birth defects we would have expected to observe similar increases in risk among mothers using progesterone for both indications. Because we predominantly observed increased associations among mothers using progesterone for threatened miscarriage but not fertility assistance, it is possible the increased associations we observed were confounded by indication (i.e. progesterone was administered for vaginal bleeding which occurred as a sequelae to the formation of a congenital anomaly. ^ No significant increased associations were observed between maternal spermicide use during pregnancy and 26 of 27 types of structural malformations. While multiple statistical tests were performed we observed first trimester maternal spermicide use to be associated with a significant increased occurrence of perimembranous ventricular septal defects (OR 2.21, 95% CI 1.16-4.21). A decreased occurrence (OR < 1.0) was observed for several categories of birth defects among mothers who conceived in the first cycle after discontinuing the use of spermicides (22 of 28) or male condoms (23 of 33). ^ Overall the percent of IUD use was similar between mothers of controls and mothers of all cases in aggregate (crude OR 1.05, 95% CI 0.61-1.84). Power was limited to detect significant associations between IUD use and birth defects, however mothers using an IUD in the month immediately prior to conception or during pregnancy were not associated with an increase of birth defects. Limb defects and amniotic band sequence previously reported to be associated with IUD use during pregnancy were not found to occur among any mothers reporting the use of an IUD during pregnancy.^

The application of latent variable models to the assessment of determinants of HIV risk behavior

Studies on the relationship between psychosocial determinants and HIV risk behaviors have produced little evidence to support hypotheses based on theoretical relationships. One limitation inherent in many articles in the literature is the method of measurement of the determinants and the analytic approach selected. ^ To reduce the misclassification associated with unit scaling of measures specific to internalized homonegativity, I evaluated the psychometric properties of the Reactions to Homosexuality scale in a confirmatory factor analytic framework. In addition, I assessed the measurement invariance of the scale across racial/ethnic classifications in a sample of men who have sex with men. The resulting measure contained eight items loading on three first-order factors. Invariance assessment identified metric and partial strong invariance between racial/ethnic groups in the sample. ^ Application of the updated measure to a structural model allowed for the exploration of direct and indirect effects of internalized homonegativity on unprotected anal intercourse. Pathways identified in the model show that drug and alcohol use at last sexual encounter, the number of sexual partners in the previous three months and sexual compulsivity all contribute directly to risk behavior. Internalized homonegativity reduced the likelihood of exposure to drugs, alcohol or higher numbers of partners. For men who developed compulsive sexual behavior as a coping strategy for internalized homonegativity, there was an increase in the prevalence odds of risk behavior. ^ In the final stage of the analysis, I conducted a latent profile analysis of the items in the updated Reactions to Homosexuality scale. This analysis identified five distinct profiles, which suggested that the construct was not homogeneous in samples of men who have sex with men. Lack of prior consideration of these distinct manifestations of internalized homonegativity may have contributed to the analytic difficulty in identifying a relationship between the trait and high-risk sexual practices. ^

The care to share HIV disclosure study - the attitudes toward and beliefs about HIV disclosure among perinatally-infected HIV-positive youth and their caregivers

HIV incidence has not changed since the introduction of the pandemic. Daily 14,000 persons are infected with HIV and 25 to 50% of the HIV-infected population and subgroups respectively are estimated to be unaware of their HIV diagnosis. Perinatally-infected HIV-positive youth, aged 13-24 years, have survived unexpectedly into adulthood, have had unique HIV disclosure experiences and now face HIV disclosure issues of adulthood and perhaps parenthood. Despite new effective HIV therapies, no HIV prevention plan exists that has diminished the rate of new HIV infections. HIV stigma and lack of universal HIV reporting laws dissuade timely HIV disclosure. Missed HIV disclosure perpetuates HIV transmission and infection. Understanding the attitudes and beliefs of HIV disclosure among perinatally-infected HIV-positive youth and their caregivers may uncover reasons to HIV disclosure delays, avoidance and intentions. The Care to Share HIV Disclosure study was designed to identify the attitudes and beliefs of HIV disclosure among HIV-positve youth (aged 13-24 years), who were infected from birth and who knew their HIV diagnosis, along with their caregivers. Twenty-six participants (15 youth and 11 caregivers) completed the theory-based questionnaires of a 21-item multiple choice survey on HIV disclosure framed in the Theory of Reasoned Action and Theory of Planned Behavior and included an additional open-ended survey that applied the Transactional Model of Stress and Coping to address youth's and caregivers' HIV disclosure experiences. Youth were found to have a selective unfavorable HIV disclosure outcome when among referents of close friends. However youth did believe in HIV partner notification. For caregivers, it mattered who disclosed the HIV illness to the youth. HIV stigma was of concern based on the youths' tendency to believe in keeping HIV a secret and their caregivers' ambivalence to HIV secrecy. However, favorable HIV disclosure outcomes were identified for both youth and caregivers the potential for HIV disclosure: when seeking HIV knowledge, when around caregivers and close family and in situations of perceived controllability as when helping others learn about HIV. These findings unveil HIV disclosure attitudes and beliefs within this population and may reveal the attributes that may inhibit or promote HIV disclosure behaviors. HIV disclosure studies that address attitudes and beliefs among larger populations of youth and HIV-infected persons are necessary to identify effective individual, group and society approaches that would promote timely, responsible and meaningful HIV disclosure methods that promote a healthy identity and interrupt HIV transmission.^

Disparities in asthma prevalence: The influence of sociodemographic and workplace factors

Asthma is a serious and continuing health problem that affects millions of Americans. Our study was conducted in response to this serious health problem and for purposes of addressing the issue of potential health disparities as outlined in Healthy People 2010. Data from sub-populations of subjects who participated in the National Health and Nutrition Examination Survey (NHANES) from 1999-2004 were used to complete the following specific aims: (1) to update nationally-based estimates of the prevalence of current and lifetime (ever) asthma among adults in the United States (U.S.) and describe by gender the relationships between potential risk factors (e.g., sociodemographics and lifestyle) and asthma; (2) to describe demographic characteristics among working adults in the U.S. and update estimates of the prevalence of asthma in this sub-population, stratified by occupation and industry; and 3) to determine the utility of adapting a population-based Job Exposure Matrix (JEM) for classifying workplace exposures to asthmagens. ^ Our findings suggest the prevalence of asthma among U.S. adults is continuing to rise, with women having a higher prevalence of asthma than men. Living below the poverty threshold, obesity, and prior history of smoking remain important determinants of asthma. Our study also adds to the increasing evidence that health care workers (HCWs) and those employed in education remain at high risk and that appropriate evaluation and control measures need to be implemented. Over 78% of HCWs and 71% of teachers in our study were females suggesting that further exploration of gender-specific risk factors of asthma in working populations is needed. ^ Our study also addressed the feasibility of adapting a population-based asthma-specific JEM to NHANES (1999-2004). We were not able to apply the asthma-specific JEM due to the broad occupational categories within NHANES. This represents a missed opportunity to examine the association between workplace exposures and asthma in U.S. working adults. However, we have identified steps that may be implemented in future population-based studies that would allow the asthma-specific JEM (and other population-based job exposure matrices) to be used in future studies of the U.S. working population.^

The role of workplace absence as an organizational mechanism in predicting employee alcohol and drug disorders

Background. EAP programs for airline pilots in companies with a well developed recovery management program are known to reduce pilot absenteeism following treatment. Given the costs and safety consequences to society, it is important to identify pilots who may be experiencing an AOD disorder to get them into treatment. ^ Hypotheses. This study investigated the predictive power of workplace absenteeism in identifying alcohol or drug disorders (AOD). The first hypothesis was that higher absenteeism in a 12-month period is associated with higher risk that an employee is experiencing AOD. The second hypothesis was that AOD treatment would reduce subsequent absence rates and the costs of replacing pilots on missed flights. ^ Methods. A case control design using eight years (time period) of monthly archival absence data (53,000 pay records) was conducted with a sample of (N = 76) employees having an AOD diagnosis (cases) matched 1:4 with (N = 304) non-diagnosed employees (controls) of the same profession and company (male commercial airline pilots). Cases and controls were matched on the variables age, rank and date of hire. Absence rate was defined as sick time hours used over the sum of the minimum guarantee pay hours annualized using the months the pilot worked for the year. Conditional logistic regression was used to determine if absence predicts employees experiencing an AOD disorder, starting 3 years prior to the cases receiving the AOD diagnosis. A repeated measures ANOVA, t tests and rate ratios (with 95% confidence intervals) were conducted to determine differences between cases and controls in absence usage for 3 years pre and 5 years post treatment. Mean replacement costs were calculated for sick leave usage 3 years pre and 5 years post treatment to estimate the cost of sick leave from the perspective of the company. ^ Results. Sick leave, as measured by absence rate, predicted the risk of being diagnosed with an AOD disorder (OR 1.10, 95% CI = 1.06, 1.15) during the 12 months prior to receiving the diagnosis. Mean absence rates for diagnosed employees increased over the three years before treatment, particularly in the year before treatment, whereas the controls’ did not (three years, x = 6.80 vs. 5.52; two years, x = 7.81 vs. 6.30, and one year, x = 11.00cases vs. 5.51controls. In the first year post treatment compared to the year prior to treatment, rate ratios indicated a significant (60%) post treatment reduction in absence rates (OR = 0.40, CI = 0.28, 0.57). Absence rates for cases remained lower than controls for the first three years after completion of treatment. Upon discharge from the FAA and company’s three year AOD monitoring program, case’s absence rates increased slightly during the fourth year (controls, x = 0.09, SD = 0.14, cases, x = 0.12, SD = 0.21). However, the following year, their mean absence rates were again below those of the controls (controls, x = 0.08, SD = 0.12, cases, x¯ = 0.06, SD = 0.07). Significant reductions in costs associated with replacing pilots calling in sick, were found to be 60% less, between the year of diagnosis for the cases and the first year after returning to work. A reduction in replacement costs continued over the next two years for the treated employees. ^ Conclusions. This research demonstrates the potential for workplace absences as an active organizational surveillance mechanism to assist managers and supervisors in identifying employees who may be experiencing or at risk of experiencing an alcohol/drug disorder. Currently, many workplaces use only performance problems and ignore the employee’s absence record. A referral to an EAP or alcohol/drug evaluation based on the employee’s absence/sick leave record as incorporated into company policy can provide another useful indicator that may also carry less stigma, thus reducing barriers to seeking help. This research also confirms two conclusions heretofore based only on cross-sectional studies: (1) higher absence rates are associated with employees experiencing an AOD disorder; (2) treatment is associated with lower costs for replacing absent pilots. Due to the uniqueness of the employee population studied (commercial airline pilots) and the organizational documentation of absence, the generalizability of this study to other professions and occupations should be considered limited. ^ Transition to Practice. The odds ratios for the relationship between absence rates and an AOD diagnosis are precise; the OR for year of diagnosis indicates the likelihood of being diagnosed increases 10% for every hour change in sick leave taken. In practice, however, a pilot uses approximately 20 hours of sick leave for one trip, because the replacement will have to be paid the guaranteed minimum of 20 hour. Thus, the rate based on hourly changes is precise but not practical. ^ To provide the organization with practical recommendations the yearly mean absence rates were used. A pilot flies on average, 90 hours a month, 1080 annually. Cases used almost twice the mean rate of sick time the year prior to diagnosis (T-1) compared to controls (cases, x = .11, controls, x = .06). Cases are expected to use on average 119 hours annually (total annual hours*mean annual absence rate), while controls will use 60 hours. The cases’ 60 hours could translate to 3 trips of 20 hours each. Management could use a standard of 80 hours or more of sick time claimed in a year as the threshold for unacceptable absence, a 25% increase over the controls (a cost to the company of approximately of $4000). At the 80-hour mark, the Chief Pilot would be able to call the pilot in for a routine check as to the nature of the pilot’s excessive absence. This management action would be based on a company standard, rather than a behavioral or performance issue. Using absence data in this fashion would make it an active surveillance mechanism. ^

AROUSAL, FATIGUE AND MENTAL PERFORMANCE: THE EFFECTS OF FASTING ON COGNITION

This study examined the effects of skipping breakfast on selected aspects of children's cognition, specifically their memory (both immediate and one week following presentation of stimuli), mental tempo, and problem solving accuracy. Test instruments used included the Hagen Central/Incidental Recall Test, Matching Familiar Figures Test, McCarthy Digit Span and Tapping Tests. The study population consisted of 39 nine-to eleven year old healthy children who were admitted for overnight stays at a clinical research setting for two nights approximately one week apart. The study was designed to be able to adequately monitor and control subjects' food consumption. The design chosen was the cross-over design where randomly on either the first or second visit, the child skipped breakfast. In this way, subjects acted as their own controls. Subjects were tested at noon of both visits, this representing an 18-hour fast.^ Analysis focused on whether or not fasting for this period of time affected an individual's performance. Results indicated that for most of the tests, subjects were not significantly affected by skipping breakfast for one morning. However, on tests of short-term central and incidental recall, subjects who had skipped breakfast recalled significantly more of the incidental cues although they did so at no apparent expense to their storing of central information. In the area of problem-solving accuracy, subjects skipping breakfast at time two made significantly more errors on hard sections of the MFF Test. It should be noted that although a large number of tests were conducted, these two tests showed the only significant differences.^ These significant results in the areas of short-term incidental memory and in problem solving accuracy were interpreted as being an effect of subject fatigue. That is, when subjects missed breakfast, they were more likely to become fatigued and in the novel environment presented in the study setting, it is probable that these subjects responded by entering Class II fatigue which is characterized by behavioral excitability, diffused attention and altered performance patterns. ^

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Proceedings of the Nineteenth Annual Biochemical Engineering Symposium

The nineteenth symposium was held at the University of Missouri–Columbia on April 22, 1989. A total of eighteen papers were scheduled for presentation, of which nine were in poster session. Finally, fifteen papers were presented and sixteen were submitted for this proceedings. It was attended by 53 participants from five institutions. A sixth group (from Colorado State University) was kept from attending the symposium due to mechanical problems on the road and we missed them. Since they worked hard at their presentations, I requested CSU-group to submit their papers for the proceedings and I am happy that they did. ContentsMathematical modelling of a flour milling system. K. Takahashi, Y. Chen, J. Hosokoschi, and L. T. Fan. Kansas State University A novel solution to the problem of plasmid segregation in continuous bacterial fermentations. K.L. Henry, R. H. Davis, and A. L. Taylor. University of Colorado Modelling of embryonic growth in avian and reptile Eggs. C.L. Krause, R. C. Seagrave, and R. A. Ackerman. Iowa State University Mathematical modeling of in situ biodegradation processes. J.C. Wu, L. T. Fan, and L. E. Erickson. Kansas State University Effect of molecular changes on starch viscosity. C.H. Rosane and V. G. Murphy. Colorado State University Analysis of two stage recombinant bacterial fermentations using a structured kinetic model. F. Miao and D. S. Kampala. University of Colorado Lactic acid fermentation from enzyme-thinned starch by Lactobacillus amylovorus. P.S. Cheng, E. L. Iannotti, R. K. Bajpai, R. Mueller, and s. Yaeger. University of Missouri–Columbia Solubilization of preoxidized Texas lignite by cell-free broths of Penicillium strains. R. Moolick, M. N. Karim, J. C. Linden, and B. L. Burback. Colorado State University Separation of proteins from polyelectrolytes by ultrafiltration. A.G. Bazzano and C. E. Glatz. Iowa State University Growth estimation and modelling of Rhizopus oligosporus in solid state fermentations. D.-H. Ryoo, V. G. Murphy, M. N. Karim, and R. P. Tengerdy. Colorado State University Simulation of ethanol fermentations from sugars in cheese whey. C.J. Wang and R. K. Bajpai. University of Missouri–Columbia Studies on protoplast fusion of B. licheniformis. B. Shi, Kansas State University Cell separations of non-dividing and dividing yeasts using an inclined settler. C.-Y. Lee, R. H. Davis, and R. A. Sclafani. University of Colorado Effect of·serum upon local hydrodynamics within an airlift column. G.T. Jones, L. E. Erickson, and L. A. Glasgow. Kansas State University Optimization of heterologous protein secretion in continuous culture. A. Chatterjee, W. F. Remirez, and R. H. Davis. University of Colorado An improved model for lactic acid fermentation. P. Yeh, R. K. Bajpai, and E. L. Iannotti. University of Missouri–Columbia

Diversity of planktonic foraminifer fauna found in 18 deep-sea cores from the North Atlantic

Greenland stadial/interstadial cycles are known to affect the North Atlantic's hydrography and overturning circulation and to cause ecological changes on land (e.g., vegetation). Hardly any information, directly expressed as diversity indices, however, exists on the impacts of these millennial-scale variations on the marine flora and fauna. We calculated three diversity indices (species richness, Shannon diversity index, Hurlbert's probability of interspecific encounter) for the planktonic foraminifer fauna found in 18 deep-sea cores covering a time span back to 60 ka. Clear differences in diversity response to the abrupt climate change can be observed and some records can be grouped accordingly. Core SO82-05 from the southern section of the subpolar gyre, the cores along the British margin and core MD04-2845 in the Bay of Biscay show two modes of diversity distribution, with reduced diversity (uneven fauna) during cold phases and the reverse (even fauna) during warm phases. Along the Iberian margin high species diversity prevailed throughout most of the glacial period. The exceptions were the Heinrich stadials when the fauna abruptly shifted from an even to an uneven or less even fauna. Diversity changes were often abrupt, but revealed a high resilience of the planktonic foraminifer faunas. The subtropical gyre waters seem to buffer the climatic effects of the Heinrich events and Greenland Stadials allowing for a quick recovery of the fauna after such an event. The current work clearly shows that planktonic foraminifer faunas quickly adapt to climate change, albeit with a reduced diversity.